Abscisic acid induces the expression of AsKIN during the recovery period of garlic cryopreservation

Identification of functional pathways and hub genes associated with the heterochronic development of sugarcane axillary buds and sett roots through multi-omics analysis

Introduction

Sugarcane is primarily propagated for large-scale agricultural production through vegetative reproduction by planting stem cuttings. Development of sprout and sett root from the cuttings is essential for sugarcane plant to adapt to the field environment. We observed asynchronous development during the sprouting of stem cuttings in two sibling sugarcane cultivars sharing the same parent in cross breeding: the axillary buds of cultivar ZZ2 (ZZ2B) sprout earlier, while the sett roots of ZZ9 (ZZ9R) emerge sooner.

Methods

Comparison of the sett root architecture, soluble sugar content, plant hormone levels and gene expression profiles during sprouting.

Results

We found that ZZ9 has a lower root cortex thickness ratio and a higher vascular cylinder thickness ratio. We also identified significant differences in the levels of soluble sugars, 3-Indolebutyric acid (IBA), N6-isopentenyladenosine (IPA), cis-Zeatin (cZ), Abscisic Acid (ABA), Gibberellin A3 (GA3), Gibberellin A7 (GA7), (±)-Jasmonic acid (JA), and N-((-)-jasmonoyl)-Sisoleucine (JA-Ile) between these cultivars. cuttings. In addition, we identified differentially expressed genes through transcriptomic analysis and discovered, via GO and KEGG enrichment analyses, that negative regulation of external stimulus response is a key to the preference of ZZ2 for early bud sprouting. The Twin-arginine translocation complex (Tat) significantly influences the preference of ZZ9's root emergence. Furthermore, weighted gene co-expression network analysis (WGCNA) revealed that specific metabolic processes in seed coat mucilage uniquely determine the asynchronous development of sett roots and axillary buds.

Discussion

These findings provide a theoretical foundation and new perspective for understand asynchronous development in sugarcane production, offering novel insights for breeding high-quality varieties.

Integrated genome-wide association and transcriptomic studies reveal genetic architecture of bulb storability of plentiful garlic germplasm resources

Garlic is a widely utilized condiment and health product. However, garlic bulbs are prone to quality deterioration resulting in decrease of economic value during postharvest. In this study, the storability of 501 garlic accessions worldwide was evaluated based on the examination of decay index (DI), decay rate, sprouting rate, and bud-to-clove ratio in two consecutive years. The DI was employed as a primary index for evaluating the storability of garlic. Among these garlic, 43 accessions exhibited strong storability with DI of 0%-5%. Phenotypic and cytological observations revealed that strong storability accessions displayed delayed sprouting and decay, a slow rate of nutrient transfer to vascular bundles. Through genome-wide association study (GWAS), 234 single-nucleotide polymorphism loci (SNPs) were associated with the storability, which were located in or near 401 genes, which were annotated the functions of resistance, storage substances transport, etc. A total of 44 genes were screened using selective sweep analysis. Transcriptomic analysis was performed at four periods after storage in the 8N035 accession with strong storability and 8N258 accession with weak storability. Compared with 8N035, the upregulated genes in the 8N258 were enriched in photosynthesis and stress response, whereas the downregulated genes were enriched in response of biotic and abiotic stress and defense response. A co-expression network and GWAS identified three hub genes as key regulatory genes. Conjoint analysis of GWAS, selective sweep, and transcriptomic analysis identified 21 important candidate genes. These findings provided excellent resources with storability and vital candidate genes regulating storability for biological breeding of garlic.

Transcriptome-wide identification of NAC (no apical meristem/Arabidopsis transcription activation factor/cup-shaped cotyledon) transcription factors potentially involved in salt stress response in garlic

Soil salinity has been an increasing problem worldwide endangering crop production and human food security. It is an ideal strategy to excavate stress resistant genes and develop salt tolerant crops. NAC (no apical meristem/Arabidopsis transcription activation factor/cup-shaped cotyledon) transcription factors have been demonstrated to be involved in salt stress response. However, relevant studies have not been observed in garlic, an important vegetable consumed in the world. In this study, a total of 46 AsNAC genes encoding NAC proteins were identified in garlic plant by transcriptome data. Phylogenetic analysis showed that the examined AsNAC proteins were clustered into 14 subgroups. Motif discovery revealed that the conserved domain region was mainly composed of five conserved subdomains. Most of the genes selected could be induced by salt stress in different tissues, indicating a potential role in salt stress response. Further studies may focus on the molecular mechanisms of the AsNAC genes in salt stress response. The results of the current work provided valuable resources for researchers aimed at developing salt tolerant crops.

Reducing Pre- and Post-Treatments in Cryopreservation Protocol and Testing Storage at -80 °C for Norway Spruce Embryogenic Cultures

Somatic embryogenesis (SE) is considered the most effective method for vegetative propagation of Norway spruce (Picea abies L. Karst). For mass propagation, a storage method that is able to handle large quantities of embryogenic tissues (ETs) reliably and at a low cost is required. The aim of the present study was to compare freezing at -80 °C in a freezer to cryopreservation using liquid nitrogen (LN) as a method for storing Norway spruce ETs. The possibility of simplifying both the pre-treatment and thawing processes in cryopreservation was also studied. The addition of abscisic acid (ABA) to the pre-treatment media and using polyethylene glycol PEG4000 instead of PEG6000 in a cryoprotectant solution were tested. Both the pre-and post-treatments on semi-solid media could be simplified by reducing the number of media, without any loss of genotype or embryo production capacity of ETs. On the contrary, the storage of ETs in a freezer at -80 °C instead of using LN was not possible, and the addition of ABA to the pre-treatment media did not provide benefits but increased costs. The lower regeneration rate after using PEG4000 instead of PEG6000 in a cryoprotectant solution in cryovials was unexpected and unwanted. The simplified pre-and post-treatment protocol will remarkably reduce the workload and costs in the mass-cryopreservation of future forest regeneration materials and in thawing the samples for mass propagations, respectively.